Barack Obama won the White House in November with the help of a majority of Catholic voters, but it didn't mean that Catholics, who in recent years had mostly sided with the GOP because of social issues, had any illusions about Obama's stance on such sensitive matters.

They fully expected that he would overturn the so-called Mexico City policy restricting family-planning funding overseas, reverse George W. Bush's ban on federal funding for embryonic-stem-cell research and move to rescind a last-minute Bush Administration "conscience clause" rule for medical providers, the latter of which he will probably do as early as next week. But they also presumed Obama would handle and communicate these weighty decisions with a delicate touch, and in that respect, the President has disappointed the crucial voting bloc. It's something Obama can ill afford, especially at time when his Administration is under constant fire from a determined group of conservative Catholics. (See new fronts in the abortion battle.)

Embryonic-stem-cell research, for instance, wasn't an issue during the presidential campaign, in large part because John McCain and Obama both support it. Candidate Obama pledged to reverse the ban on stem-cell funding, and his Inaugural Address  in which he vowed to "restore science to its rightful place"  served notice that he would not wait long to do so. So it didn't come as a surprise to Catholics when, on the morning of March 9, the President signed an Executive Order allowing research on embryonic stem cells to go forward after an eight-year halt. Obama's forceful explanation for his decision, however, took them aback.

The previous ban on research, Obama declared, was "a false choice between sound science and moral values"; Americans, he argued, should "harness the power of science to achieve our goals." (See the top 10 medical breakthroughs of 2008.)

Leaders at the U.S. Catholic Bishops Conference denounced the decision, calling it "morally wrong." And a Vatican bioethics official criticized it as "a victory of politics over ethics." But what White House advisers didn't expect was the pained anger in the reactions of far more moderate Catholics. An editorial in the liberal Catholic magazine Commonwealaccused Obama of "obfuscat[ing] the moral dilemma by resorting to imprecise talk about the supposedly self-evident authority of scientific 'facts' and the alleged ideological agenda of those opposed to embryonic-stem-cell research." At the website Beliefnet.com, religion writer David Gibson labeled the decision "Obama's Stem-Cell Flop."

The strong language used by Obama struck some observers as the sort of black-and-white rhetoric he usually avoids  and that his predecessor had embraced. Many Catholics, including New York Times columnist Peter Steinfels, embraced the critique leveled by Slate writer William Saletan (a non-Catholic). "Proponents of embryo research are insisting that because we're in a life-and-death struggle  in this case, a scientific struggle  anyone who impedes that struggle by renouncing effective tools is irrational and irresponsible," wrote Saletan. "The war on disease is like the war on terror. Either you're with science or you're against it."

The handling of the Department of Health and Human Services (HHS) rule providing conscience exceptions for health-care workers who for religious reasons refuse to dispense birth control or participate in abortion procedures has upset some Catholics for different reasons. As with the stem-cell decision, Obama's announcement that he would move toward rescinding the rule didn't come as a surprise. In addition, even Catholic leaders disagree about whether federal law provides sufficient protections without the rule, which was one of Bush's last acts in December. If scores of workers would be forced to violate their religious beliefs, ask opponents of the rule, then why did Bush wait eight years to put it in place? (Read "The Grassroots Abortion War.")

But religious advocates, led by Catholic health-care organizations, hoped to have some input into the Administration's eventual decision on the HHS rule. They submitted proposals during a 30-day comment period that ended at midnight on Friday. And they were encouraged earlier this week when the director of Obama's Office of Faith-Based and Neighborhood Partnerships, Joshua DuBois, repeatedly stressed that the White House wanted open communication and feedback from religious leaders.

The White House, however, has strongly hinted to abortion-rights advocates that the comment period was merely a formality and that Obama is expected to rescind the rule as early as next week. That has some religious leaders privately grumbling about whether their input is welcome only for those topics on which they agree with the White House. Joel Hunter, an Evangelical pastor and member of Obama's faith advisory council, told the Washington Post that reversing the rule would be "one of those things that kind of says, 'I knew it. They talk about common ground, but what they want is their own way.' "

Ordinarily, even those initial few missteps might not hurt Obama's standing among Catholics. After all, he got 54% of their votes not because of his positions on social issues but because of concerns about the economy, health care and Iraq. Indeed, Catholics are more natural partners for Democrats than has been clear over the past three decades. A Gallup poll released in late March showed that Catholics are more liberal than other Americans when it comes to accepting a wide range of matters, such as homosexuality, gambling and out-of-wedlock births, and are far more likely to oppose capital punishment.

But Obama's first few months in office have seen a sustained assault by a loose coalition of Catholic organizations and leaders who are committed to convincing their fellow church members that Obama doesn't share their values. They have strongly criticized his selection of Kansas Democratic Governor (and pro-choice Catholic) Kathleen Sebelius to be HHS Secretary and have circulated unfounded rumors that the Vatican rejected several candidates to be Obama's ambassador there. Most visibly, the right-wing Cardinal Newman Society and a number of Catholic bishops have protested the University of Notre Dame's decision to invite Obama to speak at this spring's commencement. Even Cardinal Francis George, who sat down in the Oval Office for a half-hour meeting on St. Patrick's Day that he hoped would "foster fruitful dialogue for the sake of the common good," slammed the school's action, calling it "an embarrassment to Catholics." (Notre Dame has made clear it will not rescind the invitation.)

None of these attacks should pose a serious problem for Obama. But lined up against his early moves to restore liberal social policies that many pro-life Catholics oppose, they make it easier for the President's Catholic critics to question whether he respects their values and positions.

A relatively simple way for Obama to neutralize those doubts would be to move forward with a policy to lower abortion rates, an effort his campaign pitched heavily to Catholic voters to illustrate his commitment to finding common ground with abortion opponents. A team of aides assigned to focus on abortion reduction plans to hold its first meetings with pro-life and pro-choice advocates over the next month. But it is already encountering some resistance from both sides and doesn't foresee acting on the issue in time to affect funding before the 2011 fiscal year.

Bill Clinton also benefited from Catholic backing at the polls, but he squandered some of that goodwill when those supporters concluded that he failed to carry through on his promise to reduce abortion rates. "When he said that abortion should be 'safe, legal and rare,' we all believed him," railed then Commonweal editor Margaret Steinfels after Clinton vetoed a ban on so-called partial-birth abortions. Right now, Obama is surfing impressively high approval ratings. But he can't afford to alienate those liberal and moderate Catholics who could defend him when times get tough.